AMBER Archive (2002)

Subject: Re: input format for gibbs restraints

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 13 2002 - 19:53:27 CST

On Wed, Nov 13, 2002, Jose Ramon Blas wrote:
>
> In the manual:
> ----------------------------------------------------------------
> Restraint/constraint definitions must be entered in the formatted
> form shown below, not in a namelist.
>
> Restraints/constraints are read in as pairs of lines:
>
>
> line A: IAT1,IAT2,IAT3,IAT4,IUMB,IZE,ITOR,RLMDA1,RLMDA
> FORMAT (7(I5,1X),2F10.5)
> line B: RKEQ1,REQ1,RKEQ2,REQ2,IPER,IPER2
> FORMAT (4F10.5,2I5)
>

You need to distinguish between harmonic (position) restraints, which
keep atoms from moving very far from their intial conditions (ntr=1)

and

internal restraints, which keep certain bond lengths, angles, etc. near
prescribed values (intr=1).

You have requested ntr=1 (and by default, intr=0) in your input file,
hence asking for harmonic restraints but not for internal restraints.

However, the remainder of your input is that for internal restraints (intr>0).

You should be able to fix things by
(a) changing "ntr=1" to "intr=1" in the namelist;
(b) removing the card that says "Restraints applied": internal restraints
    do not have such "title cards.

>
> My input:
> ----------------------------------------------------------------
> # FEP del monomer amb q -1
> &cntrl
> timlim=999999., ibelly=0, iewald=0,
> ntx=7, ntxo=1,
> ntb=0, iftres=1,
> nrun=41, ntt=1, temp0=298.0,
> ntp=0, taup=0.4,
> nstlim=10000, init=4, dt=0.002,
> ntc=3, ncorc=1, itimth=1,
> ntf=3, idiel=1, idsx0=-1, ioleps=0, intprt=1,
> cut=1000, scnb=2.0, scee=1.2, dielc=1.0,
> ntpr=100, ntwx=10000, ntwv=-1, ntwe=10000, isande=1,
> ntr=1,
> almda=1.00, almdel=-0.025, isldyn=-3, idifrg=1, nstmeq=5000,
> nstmul=5000, idwide=1,
> nstpe=5000, nstpa=5000,
> iperat=1, iatcmp=1,
> &end
> Restraints applied
> 10 11 13 14 0 0 0 1.00000 0.00000
> 100.00000 0.00000 100.00000 0.00000 0 0
>

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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